Publications

Preprints

  • JT Nardini, BJ Stolz, KB Flores, HA Harrington, HM Byrne. Topological data analysis distinguishes parameter regimes in the Anderson-Chaplain model of angiogenesis. https://arxiv.org/abs/2101.00523

Refereed publications in scientific journals

  • JT Nardini, RE Baker, MJ Simpson, KB Flores. Learning differential equation models from stochastic agent-based model simulations. Journal of the Royal Society Interface 18:20200987. https://royalsocietypublishing.org/doi/10.1098/rsif.2020.0987
  • A Peace, PC Frost, ND Wagner et al. (incl. KB Flores) (2021) Stoichiometric Ecotoxicology for a Multisubstance World, BioScience, biaa160. https://doi.org/10.1093/biosci/biaa160
  • J Lagergren, JT Nardini, RE Baker, MJ Simpson, KB Flores (2020) Biologically-informed neural networks guide mechanistic modeling from sparse experimental data. PLoS Computational Biology 16(12): e1008462. https://doi.org/10.1371/journal.pcbi.1008462
  • F Santiago, KB Flores, S Sindi (2020) Numerical Approaches to Division and Label Structured Population Models. Letters in Biomathematics 7(1):153–170. https://lettersinbiomath.journals.publicknowledgeproject.org/index.php/lib/article/view/395
  • J Lagergren, KB Flores, M Gilman, S Tsynkov (2020) Deep learning approach to the detection of scattering delay in radar images. Journal of Statistical Theory and Practice 15, 14. https://doi.org/10.1007/s42519-020-00149-w
  • JT Nardini, JH Lagergren, A Hawkins-Daarud, L Curtin, B Morris, EM Rutter, KR Swanson, KB Flores (2020) Learning equations from biological data with limited time samples. Bulletin of Mathematical Biology 82, 119. https://doi.org/10.1007/s11538-020-00794-z
  • S Saberi-Bosari, KB Flores, A San-Miguel (2020) Deep learning-enabled analysis reveals distinct neuronal phenotypes induced by aging and cold-shock. BMC Biology 18, 130. https://doi.org/10.1186/s12915-020-00861-w
  • J Lagergren, J Nardini, GM Lavigne, EM Rutter, KB Flores (2020) Learning partial differential equations for biological transport models from noisy data. Proceedings of the Royal Society A: Mathematical, Physical, and Engineering Sciences. Vol 476. http://doi.org/10.1098/rspa.2019.0800.
  • HT Banks, KB Flores, IG Rosen, EM Rutter, M Sirlanci, WC Thompson (2018) The prohorov metric framework and aggregate data inverse problems from random PDEs. Communications in Applied Analysis, 22(3):415-446. https://acadsol.eu/en/articles/22/3/6.pdf
  • EM Rutter, C Langdale, J Hokanson, F Hamliton, HT Tran, W Grill, KB Flores (2018) Detection of Bladder Contractions from the Activity of the External Urethral Sphincter in Rats Using Sparse Regression. IEEE Transactions on Neural Systems & Rehabilitation Engineering, https://www.doi.org/10.1109/TNSRE.2018.2854675.
  • EM Rutter, HT Banks, KB Flores (2018) Estimating intratumoral heterogeneity from spatiotemporal data. Journal of Math Biology, https://doi.org/10.1007/s00285-018-1238-6
  • J Lagergren, A Reeder, F Hamilton, RC Smith, KB Flores (2018) Forecasting and uncertainty quantification using a hybrid of mechanistic and non-mechanistic models for an age-structured population model. Bulletin of Mathematical Biology, 80(6):1578-1595. https://doi.org/10.1007/s11538-018-0421-7
  • HT Banks, KB Flores, CR Langlois, TR Serio, SS Sindi (2018) Estimating the Rate of Prion Aggregate Amplification in Yeast with a Generation and Structured Population Model. Inverse Problems in Science and Engineering, 26(2):257-279. https://doi.org/10.1080/17415977.2017.1316498
  • E Rutter, HT Banks, G LeBlanc, KB Flores (2017) Continuous structured population models for Daphnia Magna. Bulletin of Math Biology, 79(11):2627-2648. https://doi.org/10.1007/s11538-017-0344-8
  • F Hamilton, A Lloyd, KB Flores (2017) Hybrid modeling and prediction of dynamical systems. PLoS Computational Biology, 13(7): e1005655. https://doi.org/10.1371/journal.pcbi.1005655
  • HT Banks, E Collins, KB Flores, P Pershad, M Stemkovski, L Stephenson (2017) Statistical error model comparison for logistic growth of green algae (Raphidocelis subcapitata). Applied Math Letters, 64:213-222. https://doi.org/10.1016/j.aml.2016.09.006
  • HT Banks, KB Flores, S Sindi (2016) On analytical and numerical approaches to division and label structured population models. Applied Math Letters, 60:81-88. https://doi.org/10.1016/j.aml.2016.04.009
  • HT Banks, R Baraldi, KB Flores, M Stemkovski (2016) Validation of a mathematical model for green algae (Raphidocelis subcapitata) growth and implications for a coupled dynamical system with Daphnia magna. Applied Sciences, 6(5), 155 (18 pages). https://doi.org/10.3390/app6050155
  • K Adoteye, R Baraldi, KB Flores, J Nardini, HT Banks, Clayton Thompson (2015) Correlation of parameter estimators for models admitting multiple parameterizations. International Journal of Pure and Applied Mathematics, 105(3): 497-522. http://dx.doi.org/10.12732/ijpam.v105i3.16
  • HT Banks, R Baraldi, KB Flores (2015) Optimal design for minimizing uncertainty in dynamic equilibrium systems. Eurasian Journal of Mathematical and Computer Applications, 3(1): 23-47. link
  • K Adoteye, HT Banks, K Cross, S Etchyson, KB Flores, G LeBlanc, T Nguyen, C Ross, E Smith, M Stemkovski, S Stokley (2015) Statistical validation of structured population models for Daphnia magna. Mathematical Biosciences, 266:73-84. https://doi.org/10.1016/j.mbs.2015.06.003
  • The International Bumblebee Genomics Consortium (2015) The genomes of two key bumblebee species with primitive eusocial organization. Genome Biology, 16:76. https://doi.org/10.1186/s13059-015-0623-3
  • HT Banks, KB Flores, S Hu, E Rosenberg, M Buzon, X Yu, M Lichterfeld (2015) Immuno-modulatory strategies for reduction of HIV reservoir cells. Journal of Theoretical Biology, 372:146-158. https://doi.org/10.1016/j.jtbi.2015.02.006
  • HT Banks, R Baraldi, K Cross, KB Flores, C McChesney, L Poag, E Thorpe (2015) Uncertainty quantification in modeling HIV viral mechanics. Mathematical Biosciences and Engineering, 12(5):937-964. http://dx.doi.org/10.3934/mbe.2015.12.937
  • K Adoteye, HT Banks, KB Flores, GA LeBlanc (2015) Estimation of time-varying mortality rates using continuous models for Daphnia magna. Applied Math Letters, 44:12-16. https://doi.org/10.1016/j.aml.2014.12.014
  • K Adoteye, HT Banks, KB Flores (2015) Optimal design of non-equilibrium experiments for genetic network interrogation. Applied Math Letters, 40:84-89. https://doi.org/10.1016/j.aml.2014.09.013
  • HT Banks, KB Flores, K Link, L Poag, T Huffman, J Nardini (2013) A mathematical model of RNA3 recruitment in the Brome Mosaic Virus replication cycle. International Journal of Pure and Applied Mathematics, 89(2):251-274. http://doi.org/10.12732/ijpam.v89i2.9
  • RA Everett, Y Zhao, KB Flores, Y Kuang (2013) Data and implication based comparison of two Chronic Myeloid Leukemia models. Mathematical Biosciences and Engineering, 10:1501-1518. http://dx.doi.org/10.3934/mbe.2013.10.1501
  • KB Flores, F Wolschin, GV Amdam (2013) The role of methylation of DNA in environmental adaptation. Integrative and Comparative Biology, 53(2):359-72. https://doi.org/10.1093/icb/ict019
  • KB Flores (2013) A structured population modeling framework for quantifying and predicting gene expression noise in flow cytometry data. Applied Math Letters, 26(7): 794-798. https://doi.org/10.1016/j.aml.2013.03.003
  • KB Flores, F Wolschin, JJ Corneveaux, AN Allen, MJ Huentelman, GV Amdam (2012) Genome-wide association between DNA methylation and alternative splicing in an invertebrate. BMC Genomics, 13:480. https://doi.org/10.1186/1471-2164-13-480
  • KB Flores, GV Amdam. (2011) Deciphering a methylome: What can we read into patterns of DNA methylation? Journal of Experimental Biology, 214:3155-3163. http://doi.org/10.1242/jeb.059741
  • KB Flores, KP Hadeler (2010) The random walk of Azospirillum Brasilense. Journal of Biological Dynamics, 4(1): 71-85. https://doi.org/10.1080/17513750902773914

Refereed review articles in scientific journals

  • R Everett, KB Flores, N Henscheid, J Lagergren, K Larripa, D Li, JT Nardini, PTT Nguyen, EB Pitman, EM Rutter (2020) A tutorial review of mathematical techniques for quantifying tumor heterogeneity. Mathematical Biosciences and Engineering, 17(4):3660-3709. http://doi.org/10.3934/mbe.2020207
  • L-Z Wang, F Wu, KB Flores, Y-C Lai, X Wang (2016) Build to understand: synthetic approaches to biology. Integrative Biology, 8(4):394-408. https://doi.org/10.1039/C5IB00252D

Refereed articles in conference proceedings

  • EM Rutter, J Lagergren, KB Flores (2019) A Convolutional Neural Network Method for Boundary Optimization Enables Few-Shot Learning for Biomedical Image Segmentation. MICCAI 2019 Workshop: Domain Adaptation and Representation Transfer and Medical Image Learning with Less Labels and Imperfect Data. http://doi.org/10.1007/978-3-030-33391-1_22
  • EM Rutter, J Lagergren, KB Flores (2018) Automated Object Tracing for Biomedical Image Segmentation Using a Deep Convolutional Neural Network. Medical Image Computing and Computer Assisted Intervention – MICCAI 2018. http://doi.org/10.1007/978-3-030-00937-3_78
  • R Baraldi, K Cross, C McChesney, L Poag, E Thorpe, KB Flores, HT Banks (2014) Uncertainty quantification for a model of HIV-1 patient response to antiretroviral therapy interruptions. Proceedings of the 2014 American Control Conference, 2753-2758.https://doi.org/10.1109/ACC.2014.6858714

Refereed book chapters

  • A Dolezal, KB Flores, K Traynor, GV Amdam (2013) The evolution and development of eusocial insect behavior. In “Advances in Evolutionary Developmental Biology”. Jeffrey Streelman. Wiley-Blackwell, pp. 37-57. https://doi.org/10.1002/9781118707449.ch3